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Sass AM, Van Acker H, Förstner KU, Van Nieuwerburgh F, Deforce D, Vogel J, Coenye T. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC Genomics 2015; 16:775. [PMID: 26462475 PMCID: PMC4603805 DOI: 10.1186/s12864-015-1993-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. METHODS RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. RESULTS Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. CONCLUSIONS Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
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Affiliation(s)
- Andrea M Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany.
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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2
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Graindorge A, Menard A, Monnez C, Cournoyer B. Insertion sequence evolutionary patterns highlight convergent genetic inactivations and recent genomic island acquisitions among epidemic Burkholderia cenocepacia. J Med Microbiol 2011; 61:394-409. [PMID: 21980044 DOI: 10.1099/jmm.0.036822-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Burkholderia cenocepacia B&B clone was found previously to be responsible for an epidemic outbreak within an intensive care unit in France. This clone belongs to the ST32 clonal complex, which is one of the most prevalent among French cystic fibrosis patients and is known to be related to the highly virulent ET12 clonal complex. Genomic repartition biases of insertion sequences (ISs) were investigated to improve our understanding of the evolutionary events leading to B. cenocepacia diversification and the emergence of such epidemic lineages. IS were used for tracking convergent genetic inactivations and recent DNA acquisitions. B. cenocepacia IS families and subgroups were compared in terms of genetic diversity and genomic architecture using fully sequenced genomes, PCR screening and DNA blot analysis. These analyses revealed several features shared by the B&B and ET12 epidemic clones. IS elements showed a frequent localization on genomic islands (GI) and indicated convergent evolution towards inactivation of certain loci. The IS407 subgroup of the IS3 family was identified as a good indicator of recently acquired GIs in clone ET12. Several IS407 elements showed strain-specific or clonal complex-specific localizations. IS407 DNA probing of a DNA library built from the B. cenocepacia B&B epidemic clone led to the identification of a recently acquired IS407-tagged GI likely to be conjugative and integrative. The B&B clone showed significant differences in its IS architecture from that of ST32 strains isolated from Czech cystic fibrosis patients.
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Affiliation(s)
- Arnault Graindorge
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Aymeric Menard
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Claire Monnez
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Benoit Cournoyer
- Environmental Microbiology Lyon, Biological Resource Center, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France.,VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
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3
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Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D. Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 2011; 474:604-8. [PMID: 21720364 DOI: 10.1038/nature10172] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/04/2011] [Indexed: 11/09/2022]
Abstract
Prochlorococcus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. How hosts and viruses coexist in nature remains unclear, although the presence of both susceptible and resistant cells may allow this coexistence. Combined whole-genome sequencing and PCR screening technology now enables us to investigate the effect of resistance on genome evolution and the genomic mechanisms behind the long-term coexistence of Prochlorococcus and their viruses. Here we present a genome analysis of 77 substrains selected for resistance to ten viruses, revealing mutations primarily in non-conserved, horizontally transferred genes that localize to a single hypervariable genomic island. Mutations affected viral attachment to the cell surface and imposed a fitness cost to the host, manifested by significantly lower growth rates or a previously unknown mechanism of more rapid infection by other viruses. The mutant genes are generally uncommon in nature yet some carry polymorphisms matching those found experimentally. These data are empirical evidence indicating that viral-attachment genes are preferentially located in genomic islands and that viruses are a selective pressure enhancing the diversity of both island genes and island gene content. This diversity emerges as a genomic mechanism that reduces the effective host population size for infection by a given virus, thus facilitating long-term coexistence between viruses and their hosts in nature.
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Affiliation(s)
- Sarit Avrani
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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4
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Fang K, Zhao H, Sun C, Lam CMC, Chang S, Zhang K, Panda G, Godinho M, Martins dos Santos VAP, Wang J. Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC SYSTEMS BIOLOGY 2011; 5:83. [PMID: 21609491 PMCID: PMC3123600 DOI: 10.1186/1752-0509-5-83] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 05/25/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. RESULTS We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. CONCLUSIONS As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.
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Affiliation(s)
- Kechi Fang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Stevens P, van Elsas JD. A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization. Antonie van Leeuwenhoek 2010; 98:359-77. [PMID: 20467813 PMCID: PMC2935973 DOI: 10.1007/s10482-010-9450-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/20/2010] [Indexed: 01/14/2023]
Abstract
Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato.
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Affiliation(s)
- Patricia Stevens
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen, 9759 AA Haren, The Netherlands
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6
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The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol 2008; 191:261-77. [PMID: 18931103 PMCID: PMC2612433 DOI: 10.1128/jb.01230-08] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.
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7
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Bartholdson SJ, Brown AR, Mewburn BR, Clarke DJ, Fry SC, Campopiano DJ, Govan JRW. Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex. MICROBIOLOGY-SGM 2008; 154:2513-2521. [PMID: 18667584 DOI: 10.1099/mic.0.2008/019216-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysaccharide (EPS) when onion tissue was provided as the sole nutrient. EPS production was not species-specific, was observed in isolates from both clinical and environmental sources, and did not correlate with the ability to cause maceration of onion tissue. Chemical analysis suggested that the onion components responsible for EPS induction were primarily the carbohydrates sucrose, fructose and fructans. Additional sugars were investigated, and all alcohol sugars tested were able to induce EPS production, in particular mannitol and glucitol. To investigate the molecular basis for EPS biosynthesis, we focused on the highly conserved bce gene cluster thought to be involved in cepacian biosynthesis. We demonstrated induction of the bce gene cluster by mannitol, and found a clear correlation between the inability of representatives of the Burkholderia cenocepacia ET12 lineage to produce EPS and the presence of an 11 bp deletion within the bceB gene, which encodes a glycosyltransferase. Insertional inactivation of bceB in Burkholderia ambifaria AMMD results in loss of EPS production on sugar alcohol media. These novel and surprising insights into EPS biosynthesis highlight the metabolic potential of the Bcc and show that a potential virulence factor may not be detected by routine laboratory culture. Our results also highlight a potential hazard in the use of inhaled mannitol as an osmolyte to improve mucociliary clearance in individuals with cystic fibrosis.
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Affiliation(s)
- S Josefin Bartholdson
- Centre for Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK.,School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - Alan R Brown
- Centre for Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ben R Mewburn
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - David J Clarke
- School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
| | - Stephen C Fry
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | | | - John R W Govan
- Centre for Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
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8
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Galbraith EA, Antonopoulos DA, White BA. Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples. Methods Mol Biol 2008; 410:295-333. [PMID: 18642606 DOI: 10.1007/978-1-59745-548-0_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria. Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities. Through a series of hybridizations and pblymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.
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9
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Li J, Ryder C, Mandal M, Ahmed F, Azadi P, Snyder DS, Pechous RD, Zahrt T, Inzana TJ. Attenuation and protective efficacy of an O-antigen-deficient mutant of Francisella tularensis LVS. MICROBIOLOGY-SGM 2007; 153:3141-3153. [PMID: 17768257 DOI: 10.1099/mic.0.2007/006460-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Francisella tularensis is a zoonotic, Gram-negative coccobacillus that causes tularemia in humans and animals. F. tularensis subspecies tularensis (type A) and F. tularensis subspecies holarctica (type B) are antigenically similar and more virulent than Francisella novicida in humans. The genetic locus that encodes the LPS O antigen was found to be substantially different between the type B live vaccine strain (LVS) and F. novicida. One LVS-specific gene with homology to a galactosyl transferase was selected for allelic replacement using a sacB-chloramphenicol expression suicide plasmid, and recombinants were screened for colony morphology on Congo red agar that matched that of F. novicida. Two mutants (WbtI(S187Y) and WbtI(G191V)) were isolated that contained substitutions in conserved motifs in the sugar transamine/perosamine synthetase (WbtI) of the O-antigen locus, and the latter mutant was extensively tested and characterized. WbtI(G191V) grew at the same rate as the parent strain in Chamberlain's defined medium, completely lacked O antigen, was serum-sensitive but could grow in a mouse macrophage cell line, had increased resistance to sodium deoxycholate, and was highly attenuated in mice. Complementation of WbtI(G191V) with the wild-type wbtI gene in trans restored normal LPS synthesis, phenotypic properties similar to the parent, and virulence in mice. Immunization with WbtI(G191V) protected mice against a relatively low-dose intraperitoneal challenge with LVS, but was less protective against a high-dose challenge. These results indicate that complete loss of O antigen alters the surface phenotype and abrogates virulence in F. tularensis, but also compromises the induction of full protective immunity against F. tularensis infection in mice.
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Affiliation(s)
- Jiaxin Li
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Cheryl Ryder
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Manas Mandal
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Farzana Ahmed
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - D Scott Snyder
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Roger D Pechous
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas Zahrt
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas J Inzana
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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10
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Sousa SA, Moreira LM, Wopperer J, Eberl L, Sá-Correia I, Leitão JH. The Burkholderia cepacia bceA gene encodes a protein with phosphomannose isomerase and GDP-D-mannose pyrophosphorylase activities. Biochem Biophys Res Commun 2006; 353:200-6. [PMID: 17184737 DOI: 10.1016/j.bbrc.2006.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 12/04/2006] [Indexed: 11/18/2022]
Abstract
The bceA gene is part of the Burkholderia cepacia IST408 exopolysaccharide (EPS) biosynthetic cluster. It encodes a 55.3-kDa bifunctional protein (type II PMI family) with phosphomannose isomerase (PMI) and GDP-mannose pyrophosphorylase (GMP) activities. GMP activity is strongly dependent on the presence of Ca(2+) or Mn(2+), while PMI activity can use a broader variety of divalent cations (Ca(2+)>Mn(2+)>Mg(2+)>Co(2+)>Ni(2+)). The lack of a functional bceA gene does not affect EPS production yield in a non-polar insertion bceA mutant. The in silico search for putative bceA homologues revealed the presence of 2-5 bceA orthologues in the Burkholderia genomes available. This suggests that in B. cepacia IST408 putative bceA functional homologues may compensate the bceA mutation. However, the viscosity of aqueous solutions prepared with the EPS produced by the bceA mutant was significantly reduced compared with wild-type biopolymer and the mutant forms biofilms with a size reduced by 6-fold.
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Affiliation(s)
- Sílvia A Sousa
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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11
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Jones H, Ostrowski M, Scanlan DJ. A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates. Appl Environ Microbiol 2006; 72:2730-7. [PMID: 16597977 PMCID: PMC1449036 DOI: 10.1128/aem.72.4.2730-2737.2006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Picocyanobacteria of the genus Synechococcus are important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains, Synechococcus sp. strain WH8103 (clade III) and Synechococcus sp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.
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Affiliation(s)
- H Jones
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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12
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French N, Barrigas M, Brown P, Ribiero P, Williams N, Leatherbarrow H, Birtles R, Bolton E, Fearnhead P, Fox A. Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem. Environ Microbiol 2005; 7:1116-26. [PMID: 16011749 DOI: 10.1111/j.1462-2920.2005.00782.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.
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Affiliation(s)
- Nigel French
- Defra Epidemiology Fellowship Unit, Department of Veterinary Clinical Science, Faculty of Veterinary Science, Leahurst, Wirral, UK.
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13
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Bernier SP, Sokol PA. Use of suppression-subtractive hybridization to identify genes in the Burkholderia cepacia complex that are unique to Burkholderia cenocepacia. J Bacteriol 2005; 187:5278-91. [PMID: 16030222 PMCID: PMC1196026 DOI: 10.1128/jb.187.15.5278-5291.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We have previously shown differences in virulence between species of the Burkholderia cepacia complex using the alfalfa infection model and the rat agar bead chronic infection model. Burkholderia cenocepacia strains were more virulent in these two infection models than Burkholderia multivorans and Burkholderia stabilis strains. In order to identify genes that may account for the increased virulence of B. cenocepacia, suppression-subtractive hybridization was performed between B. cenocepacia K56-2 and B. multivorans C5393 and between B. cenocepacia K56-2 and B. stabilis LMG14294. Genes identified included DNA modification/phage-related/insertion sequences and genes involved in cell membrane/surface structures, resistance, transport, metabolism, regulation, secretion systems, as well as genes of unknown function. Several of these genes were present in the ET12 lineage of B. cenocepacia but not in other members of the B. cepacia complex. Virulence studies in a chronic lung infection model determined that the hypothetical YfjI protein, which is unique to the ET12 clone, contributes to lung pathology. Other genes specific to B. cenocepacia and/or the ET12 lineage were shown to play a role in biofilm formation and swarming or swimming motility.
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Affiliation(s)
- Steve P Bernier
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. N. W., Calgary, Alberta, Canada
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14
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Tsang JSH. Molecular biology of the Burkholderia cepacia complex. ADVANCES IN APPLIED MICROBIOLOGY 2004; 54:71-91. [PMID: 15251276 DOI: 10.1016/s0065-2164(04)54002-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Jimmy S H Tsang
- Molecular Microbiology Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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15
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Affiliation(s)
- Donald E Woods
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, University of Calgary Health Sciences Centre, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1.
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Glendinning KJ, Parsons YN, Duangsonk K, Hales BA, Humphreys D, Hart C, Winstanley C. Sequence divergence in type III secretion gene clusters of theBurkholderia cepaciacomplex. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09593.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Moreira LM, Videira PA, Sousa SA, Leitão JH, Cunha MV, Sá-Correia I. Identification and physical organization of the gene cluster involved in the biosynthesis of Burkholderia cepacia complex exopolysaccharide. Biochem Biophys Res Commun 2004; 312:323-33. [PMID: 14637140 DOI: 10.1016/j.bbrc.2003.10.118] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Bacteria belonging to the Burkholderia cepacia complex (BCC) are important opportunistic pathogens in patients with cystic fibrosis (CF). Since approximately 80% of the CF isolates examined produce exopolysaccharide (EPS), it was hypothesized that this EPS may play a role in the colonization and persistence of these bacteria in the CF lung. The present study describes the identification and physical organization of the EPS biosynthetic gene cluster. This bce gene cluster was identified following the isolation of three EPS-defective mutants from the highly mucoid CF isolate IST408, belonging to BCC genomovar I, based on random plasposon insertion mutagenesis and comparison of the nucleotide sequence of the interrupted genes with the available genome of Burkholderia cenocepacia J2315. This 16.2 kb cluster includes 12 genes and is located on chromosome 2. Database searches for homologous proteins and secondary structure analysis for the deduced Bce amino acid sequences revealed genes predicted to encode enzymes required for the formation of nucleotide sugar precursors, glycosyltransferases involved in the repeat-unit assembly, and other proteins involved in polymerization and export of bacterial surface polysaccharides.
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Affiliation(s)
- Leonilde M Moreira
- Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Detsika MG, Corkill JE, Magalhães M, Glendinning KJ, Hart CA, Winstanley C. Molecular typing of, and distribution of genetic markers among, Burkholderia cepacia complex isolates from Brazil. J Clin Microbiol 2003; 41:4148-53. [PMID: 12958239 PMCID: PMC193793 DOI: 10.1128/jcm.41.9.4148-4153.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone.
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Affiliation(s)
- Maria G Detsika
- Department of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool L69 3GA, United Kingdom
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